[2024-01-24 13:45:41,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference
[2024-01-24 13:45:42,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,722] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg76986fe6-723a-4191-9c6a-8a3e45d9df37/GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna.gz | prodigal -d GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/cds.fna -a GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:51,383] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:51,384] [INFO] Task started: HMMsearch
[2024-01-24 13:45:51,384] [INFO] Running command: hmmsearch --tblout GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/reference_markers.hmm GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:51,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:51,651] [INFO] Found 6/6 markers.
[2024-01-24 13:45:51,685] [INFO] Query marker FASTA was written to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/markers.fasta
[2024-01-24 13:45:51,685] [INFO] Task started: Blastn
[2024-01-24 13:45:51,685] [INFO] Running command: blastn -query GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/reference_markers.fasta -out GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:52,345] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:52,350] [INFO] Selected 13 target genomes.
[2024-01-24 13:45:52,350] [INFO] Target genome list was writen to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:52,391] [INFO] Task started: fastANI
[2024-01-24 13:45:52,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg76986fe6-723a-4191-9c6a-8a3e45d9df37/GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna.gz --refList GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/target_genomes.txt --output GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:03,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:03,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:03,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:03,797] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:46:03,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:03,797] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acinetobacter johnsonii	strain=CIP 64.6	GCA_000368045.1	40214	40214	suspected-type	True	99.9972	1195	1197	95	conclusive
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	99.9599	1194	1197	95	conclusive
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	99.9597	1191	1197	95	conclusive
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	99.9098	1092	1197	95	conclusive
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	81.6503	562	1197	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.3067	549	1197	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.6032	523	1197	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	80.3876	466	1197	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.1709	401	1197	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	80.1527	480	1197	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.0315	442	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:03,799] [INFO] DFAST Taxonomy check result was written to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:03,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:03,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:03,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/checkm_data
[2024-01-24 13:46:03,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:03,838] [INFO] Task started: CheckM
[2024-01-24 13:46:03,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/checkm_input GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/checkm_result
[2024-01-24 13:46:37,237] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:37,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:37,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:37,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:37,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/markers.fasta)
[2024-01-24 13:46:37,259] [INFO] Task started: Blastn
[2024-01-24 13:46:37,259] [INFO] Running command: blastn -query GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04d0a1a-151b-4584-b9e6-2e8bc1bb0774/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:38,225] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:38,228] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:38,228] [INFO] Target genome list was writen to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:38,247] [INFO] Task started: fastANI
[2024-01-24 13:46:38,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg76986fe6-723a-4191-9c6a-8a3e45d9df37/GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna.gz --refList GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:56,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:56,300] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:56,300] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000368045.1	s__Acinetobacter johnsonii	99.9972	1195	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	conclusive
GCF_002165305.2	s__Acinetobacter sp002165305	93.0054	987	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135205.1	s__Acinetobacter sp002135205	89.4606	939	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCF_004331175.1	s__Acinetobacter sp004331175	81.9802	554	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331255.1	s__Acinetobacter sp004331255	81.9529	548	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400735.1	s__Acinetobacter tandoii	81.6529	558	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_016599715.1	s__Acinetobacter sp002135245	81.4506	565	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_003024525.3	s__Acinetobacter cumulans	81.3149	544	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_004336635.1	s__Acinetobacter sp004336635	81.0735	574	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_003711395.1	s__Acinetobacter sp003711395	80.7869	407	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.7839	560	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.7394	542	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135335.1	s__Acinetobacter sp002135335	80.691	533	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.6767	557	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_003664645.1	s__Acinetobacter chengduensis	80.5878	523	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_001307195.1	s__Acinetobacter equi	80.5334	403	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.4968	514	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
GCF_000368145.1	s__Acinetobacter guillouiae	80.1296	480	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.4644	426	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:56,302] [INFO] GTDB search result was written to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:56,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:56,306] [INFO] DFAST_QC result json was written to GCF_000368045.1_Acin_john_CIP_64_6_V1_genomic.fna/dqc_result.json
[2024-01-24 13:46:56,306] [INFO] DFAST_QC completed!
[2024-01-24 13:46:56,306] [INFO] Total running time: 0h1m15s